From d6c7e8f5a0d0d4b564addf5b447bed6b3ba03b5e Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Thu, 5 Mar 2026 11:47:12 +0100 Subject: Do not depend on RDKit in pai test This hopefully addresses test failures observed on R-Universe. Update coverage report. --- docs/coverage/coverage.html | 338 ++++++++++++++++++++++---------------------- 1 file changed, 169 insertions(+), 169 deletions(-) (limited to 'docs/coverage/coverage.html') diff --git a/docs/coverage/coverage.html b/docs/coverage/coverage.html index 1e9d0ad..5b3b3f1 100644 --- a/docs/coverage/coverage.html +++ b/docs/coverage/coverage.html @@ -3,16 +3,16 @@ - + - + - - + + @@ -95,7 +95,7 @@ table.table-condensed { font-size: 11px; }
-

chents coverage - 34.64%

+

chents coverage - 33.77%

  • @@ -107,8 +107,8 @@ table.table-condensed {
-
- +
+
@@ -990,16 +990,16 @@ table.table-condensed { 
      if (rdkit) {
- + 126 - 1x + ! 
        if (rdkit_available) {
- + 127 - 1x + ! 
          self$get_rdkit(template = template)
@@ -1692,28 +1692,28 @@ table.table-condensed { 226 - 2x + 1x 
      available_smiles <- names(self$smiles)
227 - 2x + 1x 
      smiles_preference <- c("user", "PubChem", "PubChem_Connectivity")
228 - 2x + 1x 
      smiles_preferred_i <- min(match(available_smiles, smiles_preference))
229 - 2x + 1x 
      smiles_preferred <- smiles_preference[smiles_preferred_i]
@@ -1727,56 +1727,56 @@ table.table-condensed { 231 - 2x + 1x 
      message("Get chemical information from RDKit using ",
232 - 2x + 1x 
              smiles_preferred, " SMILES\n",
233 - 2x + 1x 
              self$smiles[smiles_preferred])
234 - 2x + 1x 
      self$rdkit <- list()
235 - 2x + 1x 
      self$mol <- rdkit_module$Chem$MolFromSmiles(self$smiles[1])
236 - 2x + 1x 
      self$rdkit$mw <- rdkit_module$Chem$Descriptors$MolWt(self$mol)
237 - 2x + 1x 
      if (!is.null(self$mw) && !is.na(self$mw)) {
238 - 2x + 1x 
        if (round(self$rdkit$mw, 1) != round(self$mw, 1)) {
@@ -1839,14 +1839,14 @@ table.table-condensed { 247 - 2x + 1x 
      rdkit_module$Chem$rdDepictor$Compute2DCoords(self$mol)
248 - 2x + 1x 
      if (!is.null(template)) {
@@ -1881,56 +1881,56 @@ table.table-condensed { 253 - 2x + 1x 
      d2d <- rdkit_module$Chem$Draw$rdMolDraw2D$MolDraw2DSVG(400L, 400L)
254 - 2x + 1x 
      d2d$DrawMolecule(self$mol)
255 - 2x + 1x 
      d2d$FinishDrawing()
256 - 2x + 1x 
      self$svg <- d2d$GetDrawingText()
257 - 2x + 1x 
      svgfile <- tempfile(fileext = ".svg")
258 - 2x + 1x 
      psfile <- tempfile(fileext = ".ps")
259 - 2x + 1x 
      writeLines(self$svg, svgfile)
260 - 2x + 1x 
      rsvg::rsvg_ps(svgfile, psfile)
@@ -1951,21 +1951,21 @@ table.table-condensed { 263 - 2x + 1x 
      ps_font_line <- grep("Tm$", readLines(psfile), value = TRUE)[1]
264 - 2x + 1x 
      ps_font_size <- gsub(" .*$", "", ps_font_line)
265 - 2x + 1x 
      self$Pict_font_size = as.numeric(ps_font_size)
@@ -1986,35 +1986,35 @@ table.table-condensed { 268 - 2x + 1x 
      xmlfile <- tempfile(fileext = ".xml")
269 - 2x + 1x 
      PostScriptTrace(psfile, outfilename = xmlfile)
270 - 2x + 1x 
      unlink(paste0("capture", basename(psfile)))
271 - 2x + 1x 
      self$Picture <- readPicture(xmlfile)
272 - 2x + 1x 
      unlink(c(xmlfile, psfile, svgfile))
@@ -4690,126 +4690,126 @@ table.table-condensed { 654 - 
#' # On Travis, we get a certificate validation error,
+ 
#' atr <- pai$new("atrazine")
655 - 
#' # likely because the system (xenial) is so old,
+ 
#' print(atr)
656 - 
#' # therefore don't run this example on Travis
+ 
#' if (!is.null(atr$Picture)) {
657 - 
#' if (Sys.getenv("TRAVIS") == "") {
+ 
#'   plot(atr)
658 - 
#'
+ 
#' }
659 - 
#' atr <- pai$new("atrazine")
+ 
#' # We can also define pais that are not found on the BCPC site
660 - 
#' print(atr)
+ 
#' decanol <- pai$new("1-Decanol")
661 - 
#' if (!is.null(atr$Picture)) {
+ 
#' print(decanol)
662 - 
#'   plot(atr)
+ 
pai <- R6Class("pai",
663 - 
#' }
+ 
  inherit = chent,
664 - 
#'
+ 
  public = list(
665 - 
#' }
+ 

                     
                   
                   
                     666
                     
                     
-                      
pai <- R6Class("pai",

+                      
    #' @field iso ISO common name of the active ingredient according to ISO 1750

                     
                   
                   
                     667
                     
                     
-                      
  inherit = chent,

+                      
    iso = NULL,

                     
                   
                   
                     668
                     
                     
-                      
  public = list(

+                      

                     
                   
                   
                     669
                     
                     
-                      

+                      
    #' @field bcpc Information retrieved from the BCPC compendium available online

                     
                   
                   
                     670
                     
                     
-                      
    #' @field iso ISO common name of the active ingredient according to ISO 1750

+                      
    #' at <pesticidecompendium.bcpc.org>

                     
                   
                   
                     671
                     
                     
-                      
    iso = NULL,

+                      
    bcpc = NULL,

                     
                   
                   
@@ -4822,603 +4822,603 @@ table.table-condensed {
                   
                     673
                     
-                    
-                      
    #' @field bcpc Information retrieved from the BCPC compendium available online

-                    
-                  
-                  
-                    674
-                    
-                    
-                      
    #' at <pesticidecompendium.bcpc.org>

-                    
-                  
-                  
-                    675
-                    
-                    
-                      
    bcpc = NULL,

-                    
-                  
-                  
-                    676
-                    
-                    
-                      

-                    
-                  
-                  
-                    677
-                    
                     
                       
    #' @description

                     
                   
                   
-                    678
+                    674
                     
                     
                       
    #' Create a new pai object

                     
                   
                   
-                    679
+                    675
                     
                     
                       
    #' @param iso The ISO common name to be used in the query of the

                     
                   
                   
-                    680
+                    676
                     
                     
                       
    #' BCPC compendium

                     
                   
                   
-                    681
+                    677
                     
                     
                       
    #' @param identifier Alternative identifier used for querying pubchem

                     
                   
                   
-                    682
+                    678
                     
                     
                       
    #' @param smiles Optional user provided SMILES code

                     
                   
                   
-                    683
+                    679
                     
                     
                       
    #' @param inchikey Optional user provided InChI Key

                     
                   
                   
-                    684
+                    680
                     
                     
                       
    #' @param bcpc Should the BCPC compendium be queried?

                     
                   
                   
-                    685
+                    681
                     
                     
                       
    #' @param pubchem Should an attempt be made to retrieve chemical

                     
                   
                   
-                    686
+                    682
                     
                     
                       
    #' information from PubChem via the webchem package?

                     
                   
                   
-                    687
+                    683
                     
                     
                       
    #' @param pubchem_from Possibility to select the argument

                     
                   
                   
-                    688
+                    684
                     
                     
                       
    #' that is used to query pubchem

                     
                   
                   
-                    689
+                    685
                     
                     
                       
    #' @param rdkit Should an attempt be made to retrieve chemical

                     
                   
                   
-                    690
+                    686
                     
                     
                       
    #' information from a local rdkit installation via python

                     
                   
                   
-                    691
+                    687
                     
                     
                       
    #' and the reticulate package?

                     
                   
                   
-                    692
+                    688
                     
                     
                       
    #' @param template An optional SMILES code to be used as template for RDKit

                     
                   
                   
-                    693
+                    689
                     
                     
                       
    #' @param chyaml Should we look for a identifier.yaml file in the working

                     
                   
                   
-                    694
+                    690
                     
                     
                       
    initialize = function(iso, identifier = iso,

                     
                   
                   
-                    695
+                    691
                     
                     
                       
      smiles = NULL, inchikey = NULL, bcpc = TRUE,

                     
                   
                   
-                    696
+                    692
                     
                     
                       
      pubchem = TRUE, pubchem_from = 'auto',

                     
                   
                   
-                    697
+                    693
                     
                     
                       
      rdkit = TRUE, template = NULL,

                     
                   
                   
-                    698
+                    694
                     
                     
                       
      chyaml = FALSE)

                     
                   
                   
-                    699
+                    695
                     
                     
                       
    {

                     
                   
                   
-                    700
+                    696
                     
                     
                       

                     
                   
                   
-                    701
+                    697
                     1x
                     
                       
      if (!is.null(inchikey)) {

                     
                   
                   
-                    702
+                    698
                     !
                     
                       
        self$inchikey = inchikey

                     
                   
                   
-                    703
+                    699
                     !
                     
                       
        attr(self$inchikey, "source") <- "user"

                     
                   
                   
-                    704
+                    700
                     
                     
                       
      }

                     
                   
                   
-                    705
+                    701
                     
                     
                       

                     
                   
                   
-                    706
+                    702
                     1x
                     
                       
      if (!missing(iso) & bcpc) {

                     
                   
                   
-                    707
+                    703
                     1x
                     
                       
        message("Querying BCPC for ", identifier, " ...")

                     
                   
                   
-                    708
+                    704
                     1x
                     
                       
        bcpc_result = webchem::bcpc_query(identifier, from = "name")

                     
                   
                   
-                    709
+                    705
                     
                     
                       

                     
                   
                   
-                    710
+                    706
                     
                     
                       
        # Use first element of list, as we passed a query of length one

                     
                   
                   
-                    711
+                    707
                     1x
                     
                       
        if (is.na(bcpc_result[[1]][1])) {

                     
                   
                   
-                    712
+                    708
                     !
                     
                       
          message("Common name ", identifier, " is not known at the BCPC compendium, trying PubChem")

                     
                   
                   
-                    713
+                    709
                     
                     
                       
        } else {

                     
                   
                   
-                    714
+                    710
                     1x
                     
                       
          self$bcpc = bcpc_result[[1]]

                     
                   
                   
-                    715
+                    711
                     1x
                     
                       
          self$iso = self$bcpc$cname

                     
                   
                   
-                    716
+                    712
                     1x
                     
                       
          attr(self$iso, "source") <- "bcpc"

                     
                   
                   
-                    717
+                    713
                     1x
                     
                       
          attr(self$iso, "status") <- self$bcpc$status

                     
                   
                   
-                    718
+                    714
                     1x
                     
                       
          bcpc_ik = self$bcpc$inchikey

                     
                   
                   
-                    719
+                    715
                     1x
                     
                       
          if (length(bcpc_ik) == 1 && !is.na(bcpc_ik)) {

                     
                   
                   
-                    720
+                    716
                     1x
                     
                       
            if (is.null(self$inchikey)) {

                     
                   
                   
-                    721
+                    717
                     1x
                     
                       
              self$inchikey = substr(self$bcpc$inchikey, 1, 27)

                     
                   
                   
-                    722
+                    718
                     1x
                     
                       
              attr(self$inchikey, "source") <- "bcpc"

                     
                   
                   
-                    723
+                    719
                     
                     
                       
            } else {

                     
                   
                   
-                    724
+                    720
                     !
                     
                       
              if (bcpc_ik == self$inchikey) {

                     
                   
                   
-                    725
+                    721
                     !
                     
                       
                attr(self$inchikey, "source") = c(attr(self$inchikey, "source"), "bcpc")

                     
                   
                   
-                    726
+                    722
                     
                     
                       
              } else {

                     
                   
                   
-                    727
+                    723
                     !
                     
                       
                warning("InChIKey ", self$inchikey, " differs from ", bcpc_ik, " obtained from bcpc.org")

                     
                   
                   
-                    728
+                    724
                     
                     
                       
              }

                     
                   
                   
-                    729
+                    725
                     
                     
                       
            }

                     
                   
                   
-                    730
+                    726
                     
                     
                       
          }

                     
                   
                   
-                    731
+                    727
                     
                     
                       
        }

                     
                   
                   
-                    732
+                    728
                     
                     
                       
      }

                     
                   
                   
-                    733
+                    729
                     
                     
                       

                     
                   
                   
-                    734
+                    730
                     
                     
                       
      # Set pubchem_from if not specified

                     
                   
                   
-                    735
+                    731
                     1x
                     
                       
      if (pubchem_from == 'auto') {

                     
                   
                   
-                    736
+                    732
                     1x
                     
                       
        pubchem_from = 'name'

                     
                   
                   
-                    737
+                    733
                     1x
                     
                       
        if (!is.null(self$inchikey)) {

                     
                   
                   
-                    738
+                    734
                     1x
                     
                       
          pubchem_from = 'inchikey'

                     
                   
                   
-                    739
+                    735
                     
                     
                       
        }

                     
                   
                   
-                    740
+                    736
                     
                     
                       
      }

                     
                   
                   
-                    741
+                    737
                     
                     
                       

                     
                   
                   
-                    742
+                    738
                     1x
                     
                       
      super$initialize(identifier = identifier,

                     
                   
                   
-                    743
+                    739
                     1x
                     
                       
        smiles = smiles, inchikey = self$inchikey,

                     
                   
                   
-                    744
+                    740
                     1x
                     
                       
        pubchem = pubchem, pubchem_from = pubchem_from,

                     
                   
                   
-                    745
+                    741
                     1x
                     
                       
        rdkit = rdkit, template = template, chyaml = chyaml)

                     
                   
                   
-                    746
+                    742
                     
                     
                       

                     
                   
                   
-                    747
+                    743
                     1x
                     
                       
      invisible(self)

                     
                   
                   
-                    748
+                    744
                     
                     
                       
    }

                     
                   
                   
-                    749
+                    745
                     
                     
                       
  )

                     
                   
                   
-                    750
+                    746
                     
                     
                       
)

                     
                   
                   
-                    751
+                    747
                     
                     
                       

                     
                   
                   
-                    752
+                    748
                     
                     
                       
#' Printing method for pai objects (pesticidal active ingredients)

                     
                   
                   
-                    753
+                    749
                     
                     
                       
#'

                     
                   
                   
-                    754
+                    750
                     
                     
                       
#' @param x The chent object to be printed

                     
                   
                   
-                    755
+                    751
                     
                     
                       
#' @param ... Further arguments for compatibility with the S3 method

                     
                   
                   
-                    756
+                    752
                     
                     
                       
#' @export

                     
                   
                   
-                    757
+                    753
                     
                     
                       
print.pai = function(x, ...) {

                     
                   
                   
-                    758
+                    754
+                    !
+                    
+                      
  if (is.null(x$iso)) {

+                    
+                  
+                  
+                    755
                     !
                     
-                      
  cat("<pai> with ISO common name $iso", x$iso, "\n")

+                      
    cat("<pai> without ISO common name\n")

+                    
+                  
+                  
+                    756
+                    
+                    
+                      
  } else {

+                    
+                  
+                  
+                    757
+                    !
+                    
+                      
    cat("<pai> with ISO common name $iso", x$iso, "\n")

+                    
+                  
+                  
+                    758
+                    
+                    
+                      
  }

                     
                   
                   
-- 
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